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Plants and microorganisms constantly associate in an astonishing diversity of interactions, ranging from parasitism to mutualism. During the most intimate of the mutualistic associations, the symbionts colonize the plant cells intracellularly, forming an interface where active nutrient exchanges occur. These associations are thought to be as ancient as the land plants themselves, and to have diversified together with the diversification of the plant lineage. The molecular mechanisms responsible for the origin of these intracellular association and their subsequent diversification remain poorly understood, although this knowledge would be pivotal to engineer novel symbioses in crops. Using comparative phylogenomics on species covering the entire plant lineage, newly developed comparative transcriptomic methods, biochemical and reverse genetic approaches in diverse plant species we have identified key molecular events that allowed these mutualistic association to form and diversify.